Helicon

Tools for cryo-EM analysis of helical structures, such as amyloid filaments and other helical assemblies. Helicon finds the helical parameters (twist, rise, symmetry) from 2D images or 3D maps, relates 2D classes to the filaments they came from, and reconstructs a 3D map from a single 2D image or from a set of 2D classes.

It comes as command-line programs, a file viewer, and a set of web apps that run in your browser, on your own computer or on a cloud server. You can try the web apps online without installing anything.

Quick start

Helicon needs Python 3.13 or newer. Use a fresh virtual or conda environment, as it pulls in many packages.

pip install "helicon[shiny]"     # the command-line programs and the web apps
helicon                          # opens the web apps, on their Home tab
helicon --help                   # lists all programs

To get the newest development code instead of the latest release:

pip install "helicon[shiny] @ git+https://github.com/jianglab/helicon"

Choosing what to install

The plain pip install helicon gives the command-line programs. Add what you need in square brackets, separated by commas, e.g. helicon[shiny,gui].

Extra	Adds
shiny	the web apps (helicon webApps, or just helicon)
gui	the display file viewer (napari, PySide6, pyqtgraph)
streamlit	the Streamlit apps (ctfSimulation, map2seq, procart)
all	shiny, streamlit, gui and the curvelet extras
test	what the test suite needs, for developers

Keeping up to date

helicon --version        # the release and the git commit it was built from
helicon update --check   # is there a newer release?
helicon update           # install it

Only releases count, not the commits between them. helicon update also works for a git checkout (pip install -e): it moves the checkout forward to the newest release tag, and stops if you have uncommitted changes.

What is included

Web apps

Start them with helicon (or helicon webApps). Each tab works on its own.

Tab	What it does
AbInitio3D	Reconstruct a 3D map from a set of 2D classes, with the twist found by a phase fit
Denovo3D	De novo helical indexing and 3D reconstruction from a single 2D image
HelicalPitch	Determine the helical pitch and twist from 2D classification results
HILL	Helical indexing with Fourier-Bessel layer lines (power spectra and phase differences)
HI3D	Helical indexing by cylindrical projection of a 3D map
HelicalProjection	Compare 2D images with projections of helical structures from the EMDB
HelicalLattice	Convert between a 2D lattice and a helical lattice
WhereIsMyClass	Map 2D classes back to the helical tube/filament images they contain

Command-line programs

Program	What it does
cryosparc	Talk to a CryoSPARC server and run image analysis tasks
images2star	Analyze and transform datasets and save them as a RELION star file
proc3d	Analyze and transform 3D maps
trueFSC	Compute the True FSC curve with an optimal mask and phase randomization
update	Update Helicon to the newest release

Viewer and other apps

Program	Needs	What it does
display	gui	A file browser for images, maps, star, bild, eps, pdf, html and text files
ctfSimulation	streamlit	Simulate 1D and 2D TEM contrast transfer functions
map2seq	streamlit	Find the protein sequence that best explains a 3D density map
procart	streamlit	Plot cartoon illustrations of residue properties of amyloid atomic models

Run any of them with -h for its options, for example helicon images2star -h.

Documentation

• Documentation at Read the Docs: for users
• Helicon on DeepWiki: for developers
• Project page

Citation

If Helicon is useful in your work, please cite:

Li, D., Zhang, X., Jiang, W., 2025. Helicon: Helical parameter determination and 3D reconstruction from one image. Journal of Structural Biology 217, 108256. doi:10.1016/j.jsb.2025.108256

@article{li2025helicon,
  author  = {Li, D. and Zhang, X. and Jiang, W.},
  title   = {Helicon: Helical parameter determination and 3D reconstruction from one image},
  journal = {Journal of Structural Biology},
  volume  = {217},
  pages   = {108256},
  year    = {2025},
  doi     = {10.1016/j.jsb.2025.108256}
}

Development

git clone https://github.com/jianglab/helicon.git
cd helicon
pip install -e ".[all,test]"
pytest

The version comes from the release tags (v2026.10), so helicon --version in a checkout shows the commits since the last tag and the commit hash. See AGENTS.md for the code layout and conventions. Bugs and feature requests go to the issue tracker.

License

MIT